The federal government is cracking down on half a dozen Maine hospitals for high rates of complications and infections.

The six Maine facilities are among 721 hospitals nationally with high rates of infections and other patient injuries that will see their payments cut under the federal Medicare program, according to an analysis by Kaiser Health News. The crackdown is the government’s toughest effort to date aimed at reducing avoidable medical errors.

Medicare will cut payments to the hospitals by 1 percent over the fiscal year that began Oct. 1 and ends in September 2015. The federal Centers for Medicare and Medicaid Services in June released a preliminary list of hospitals likely to face penalties, followed by a confirmed list on Thursday.

In Maine, some of the state’s largest hospitals face lowered payments. The six penalized hospitals are Maine Medical Center in Portland, Eastern Maine Medical Center in Bangor, MaineGeneral Medical Center in Augusta, St. Mary’s Regional Medical Center in Lewiston, Inland Hospital in Waterville and The Aroostook Medical Center in Presque Isle.

The penalties, estimated to total $373 million nationally, will hit academic medical centers particularly hard, with about half punished, Kaiser found. Hospitals that treat a high volume of low-income patients also are more likely to be assessed penalties, as are large hospitals and those located in cities.

The federal government looked at eight avoidable patient injuries — including blood clots, bed sores, accidental falls after surgery and collapsed lung — that result from medical treatment. It also examined urinary tract infections from catheters and bloodstream infections in patients who had central lines, or catheters, placed in major veins. Medicare assigned each hospital a score on a scale of 1 to 10. Hospitals in the top quarter — with a total score above 7 — face penalties.

About 1,400 hospitals are exempt from penalties, including small “critical access hospitals” located in rural areas. Of Maine’s 38 hospitals, 16 are critical access facilities.

Preventing infections and mistakes has become a top priority for hospitals. Preventable hospital errors are the third-leading cause of death in the U.S., claiming the lives of up to 440,000 patients per year, according to a landmark September 2013 study published in the Journal of Patient Safety. But hospitals are making progress, with a recent federal report showing about 50,000 people are alive today because hospitals committed 17 percent fewer medical errors in 2013 than in 2010.

Hospital officials argue that facilities treating the sickest patients and those that identify infections properly may score worse.

St. Mary’s recorded three urinary tract infections from catheters and three central-line bloodstream infections over the review period, an unusually high number, according to Betsey Shew, director of performance improvement and case management. So far this year, the hospital has reported none of those infections, she said.

“Some of those were just incredibly sick patients,” Shew said.

St. Mary’s reviewed its numbers in June after learning the hospital made the preliminary list of penalized facilities, she said. Some patient results were improperly categorized as hospital-acquired complications, possibly because medical coders misinterpreted physicians’ documentation of surgeries and other procedures, she said. The hospital now double checks the data.

The Medicare penalty will cost St. Mary’s an estimated $100,000, Shew said.

Dr. Robert Thompson, senior vice president and chief medical officer for Eastern Maine Healthcare Systems — the parent organization to EMMC, Inland and The Aroostook Medical Center — said Medicare based the penalties on dated information, with some of it reported in 2011.

“These ratings do not reflect our present performance, and incidences of infection and injury at EMHS have declined since this data was initially released last spring,” he said in a statement. “EMHS takes all potential harm seriously. We are continually seeking to improve through partnership with our doctors, nurses, health care workers, and our patients and families across our region.”

MaineGeneral also cited dated information, saying the serious complications data was collected well before the hospital consolidated inpatient services at the new Alfond Center for Health in November 2013. Private rooms at the new hospital help to limit infections, and the consolidation allowed MaineGeneral to streamline processes, significantly reducing urinary tract infections from catheters, according to spokeswoman Joy Leach.

“Patient health and safety is the number one goal at MaineGeneral,” she said. “Quality improvement is something we strive for at every level.”

Maine Medical Center reduced central-line infections by 50 percent compared with last year by following safety steps supported by medical evidence, such as daily antiseptic baths for patients and regular dressing changes, said Dr. Josh Cutler, vice president of quality and safety.

“We’re disappointed that we don’t measure up better in this report, but I think that we have known and we do know why that is and put a lot of effort into these areas of concern,” he said.

Cutler shares some of the doubts other hospital officials expressed about the validity of Medicare’s data, including whether the government accurately accounted for complications among sicker populations at some hospitals. But that skepticism is no excuse to write off the possibility that a hospital must improve, he said.

“The reality is we just want to avoid hurting our patients,” Cutler said.